@jbrowse/plugin-breakpoint-split-view 2.17.0 → 3.0.0

package/esm/BreakpointSplitView/util.d.ts

@@ -1,5 +1,7 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { LayoutRecord } from './model';
+import type { LayoutRecord } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 type LGV = LinearGenomeViewModel;
 interface Display {
     height: number;
@@ -7,6 +9,7 @@ interface Display {
     SNPCoverageDisplay?: {
         height: number;
     };
+    searchFeatureByID?: (str: string) => LayoutRecord;
 }
 interface Track {
     displays: Display[];
@@ -16,4 +19,11 @@ export declare function getPxFromCoordinate(view: LGV, refName: string, coord: n
 export declare function yPos(trackId: string, level: number, views: LGV[], tracks: Track[], c: LayoutRecord, getYPosOverride?: (trackId: string, level: number) => number): number;
 export declare const useNextFrame: (variable: unknown) => void;
 export declare function intersect<T>(cb: (l: T) => string, a1?: T[], a2?: T[], ...rest: T[][]): T[];
+export declare function getClip(cigar: string, strand: number): number;
+export declare function calc(track: Track, f: Feature): LayoutRecord | undefined;
+export declare function getBlockFeatures(model: {
+    views: LinearGenomeViewModel[];
+}, track: {
+    configuration: AnyConfigurationModel;
+}): Promise<Feature[][] | undefined>;
 export {};

package/esm/BreakpointSplitView/util.js

@@ -1,5 +1,6 @@
-import { useState, useEffect } from 'react';
-import { clamp } from '@jbrowse/core/util';
+import { useEffect, useState } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import { clamp, getSession } from '@jbrowse/core/util';
 const [, TOP, , BOTTOM] = [0, 1, 2, 3];
 function cheight(chunk) {
     return chunk[BOTTOM] - chunk[TOP];
@@ -14,7 +15,6 @@ export function getPxFromCoordinate(view, refName, coord) {
     var _a;
     return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
 }
-// get's the yposition of a layout record in a track
 export function yPos(trackId, level, views, tracks, c, getYPosOverride) {
     const display = tracks[level].displays[0];
     const min = 0;
@@ -29,21 +29,44 @@ export function yPos(trackId, level, views, tracks, c, getYPosOverride) {
         heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
         display.scrollTop);
 }
-// we combo a useEffect and useState combo to force rerender on snap changing.
-// the setup of this being a useEffect+useState makes it re-render once the
-// useEffect is called, which is generally the "next frame". If we removed the
-// below use
 export const useNextFrame = (variable) => {
     const [, setNextFrameState] = useState();
     useEffect(() => {
         setNextFrameState(variable);
     }, [variable]);
 };
-// https://stackoverflow.com/a/49186706/2129219 the array-intersection package
-// on npm has a large kb size, and we are just intersecting open track ids so
-// simple is better
 export function intersect(cb, a1 = [], a2 = [], ...rest) {
     const ids = new Set(a2.map(elt => cb(elt)));
     const a12 = a1.filter(value => ids.has(cb(value)));
     return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
 }
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+export function getClip(cigar, strand) {
+    return strand === -1
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
+}
+export function calc(track, f) {
+    var _a, _b;
+    return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
+}
+export async function getBlockFeatures(model, track) {
+    var _a;
+    const { views } = model;
+    const { rpcManager, assemblyManager } = getSession(model);
+    const assemblyName = (_a = model.views[0]) === null || _a === void 0 ? void 0 : _a.assemblyNames[0];
+    if (!assemblyName) {
+        return undefined;
+    }
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        return undefined;
+    }
+    const sessionId = track.configuration.trackId;
+    return Promise.all(views.map(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(track, ['adapter']),
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+    })).flat()));
+}

package/esm/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class BreakpointSplitViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/vcf": "^5.0.9",
+    "@gmod/vcf": "^6.0.0",
     "@mui/icons-material": "^6.0.0",
     "@types/file-saver": "^2.0.1",
     "file-saver": "^2.0.0"
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }